Covid-19 Tedavisi İçin Rna-Bağımlı Rna Polimeraz(RDRP) İnhibitörlerinin Sanal Ligand Taraması Yöntemiyle Tasarlanması
Özet
The COVID-19 pandemic, which started in December 2019 in Wuhan, China, has since become a global outbreak. Consequently, the virus that causes COVID-19 has been named SARS-CoV-2. According to data from the World Health Organization (WHO), the number of people infected worldwide has exceeded 775 million, with over 7.7 million deaths. In our country, over 17 million cases have been reported, with more than 100,000 deaths. Currently, there are 8 drugs approved by the European Medicines Agency (EMA) and 3 drugs approved by the United States Food and Drug Administration (USFDA) for the treatment of COVID-19. In addition to drug treatments, there are 5 vaccines that have received approval and are in use.
All coronaviruses contain three structural proteins on their membranes: the spike (S) protein, the membrane (M) protein, and the envelope (E) protein. In addition to these proteins, the viral genetic material RNA comprises four functional proteins: papain-like protease (PLpro), 3-chymotrypsin-like protease (3CLpro), RNA-dependent RNA polymerase (RdRp), and helicase. Important drug targets for new inhibitor research in COVID-19 treatment include PLpro, 3CLpro, RdRp, and the S protein. The selected drug target for this thesis is the RdRp enzyme. There are two inhibitors interacting with the RdRp enzyme: Remdesivir and Molnupiravir.
The RdRp enzyme is responsible for the transcription and replication of the RNA strand, the genetic material of the SARS-CoV-2 virus. Due to this role, the RdRp enzyme is a highly significant target. The RdRp enzyme consists of the palm, fingers, and thumb regions, with the active site located in the palm region. The active site comprises seven segments. Inhibitors that aim to bind to the active site of the RdRp enzyme typically covalently attach to the enzyme's substrate structure. The motif B region within the enzyme's active site stabilizes the substrate structure. Enzyme inhibition can be achieved by secondary interactions within this region.
This thesis study includes four computational processes: validation, molecular docking, virtual ligand screening, and ADME/Tox (absorption-distribution-metabolism-excretion/toxicity). In the first phase, validation studies were performed using the Autodock Vina program for the interaction of nucleotide-free molecules with the motif B region of the SARS-CoV-2 RdRp enzyme with the 7D4F PDB coded protein-ligand complex and its Suramin ligand. For nucleotide molecules, validation was conducted for the interaction with the motif F region of the SARS-CoV-2 RdRp enzyme using the 7BV2 PDB coded protein-ligand complex and its Remdesivir Triphosphate ligand. Re-docking calculations yielded an RMSD value of 1.878 Å for the 7D4F PDB coded protein, indicating the method's suitability with a value below 2 Å. The calculated Ki value for the ligand was found to be 1.12 nM. For the 7BV2 PDB coded protein, an RMSD value of 1.914 Å was obtained, also indicating method suitability with a value below 2 Å. The calculated Ki value for the ligand was found to be 1.45 nM.
In the second phase, molecular docking using the Autodock Vina program was performed for 10 nucleotide antiviral drugs, 24 flavonoids, and 1 non-nucleotide molecule (Suramin) used in the treatment of Zaire Ebolavirus and Zika virus. These molecules were targeted to bind to the motif B region in the active site of RdRp, responsible for RNA stabilization.
In the third phase, a virtual ligand screening was conducted in the PubChem database, resulting in a dataset of 413 molecules subjected to multiple molecular dockings. The 20 molecules with the highest affinity values were identified.
In the final phase, ADME and toxicity (absorption-distribution-metabolism-excretion/toxicity) calculations were performed for the top 20 molecules. The molecules that passed the ADME/Tox tests were determined, completing the study. These identified molecules could be effective as RdRp enzyme inhibitors in antiviral drug design for the COVID-19 pandemic and contribute significantly to the discovery of lead compounds.
